PhD Position in Scientific Computing
Uppsala University Department of Information Technology

PhD student in Scientific Computing focusing on Deep Learning for Agricultural Genomics

Published: 2021-04-29

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 45,000 students, more than 7,000 employees and a turnover of around SEK 7 billion.

The Department of Information Technology has a leading position in research and all levels of higher education. Today the department has 280 employees, including 120 academic staff and 110 full-time PhD students. The Department comprises research and education in a spectrum of areas within Computer Science, Information Technology and Scientific Computing. More than 4000 students take one or several courses offered by the Department each year.

The position is hosted by the Division of Scientific Computing within the Department of Information Technology. As one of the world’s largest focused research environments in Scientific Computing the research and education has a unique breadth, with large activities in classical scientific computing areas such as mathematical modeling, development and analysis of algorithms, scientific software development and high-performance computing. The division is currently in an expansive phase in new emerging areas such as cloud and fog computing, data science, and artificial intelligence, where it plays key roles in several new strategic initiatives at the University.

Our PhD programs in scientific computing has resulted in over 80 completed PhD theses over the years. Several PhD alumni in Scientific Computing from Uppsala University are successful practitioners in the field, in industry as well as in academia.

Project description: The PhD position offered is connected to a project grant to Carl Nettelblad. The project focus is the development and usage of artificial intelligence models for discovering population structure and predicting production traits in plant and animal breeding. This work is partially conducted in collaboration with industry partners. The development of more advanced methodology can promote diversity preservation efforts relating to historical local varieties.

We create our own models for these applications, since there are no neural networks that perform well in this space. There is a preprint available describing our foundational model, with applications to human genome data instead. This is an interdisciplinary project. Previous knowledge of genetics is not a requirement, but the successful completion of the project will require an interest in the application area. Interest and knowledge relating to neural network models and numerical optimization are crucial to the project.

Duties: The duties of a PhD student are primarily directed at their own research education, which lasts four years. The work may also involve, to a limited extent (maximum 20%) other departmental duties, such as teaching undergraduate courses and administrative tasks – in which case the position may be extended to a maximum of five years.

Requirements: A PhD position at the Division requires a Master of Science or equivalent in a field that is relevant to the topic of the PhD thesis, good communication skills and excellent study results, as well as sufficient proficiency in oral and written English. Knowledge and experience in scientific programming, numerical optimization, and deep learning are of additional importance. 

Additional qualifications: Basic knowledge of genetics in eukaryote organisms is considered to be an advantage.

Application: Your application should include

  • a personal letter describing your background, relevant qualification, research interests and how you see that your background would contribute to the specific project.
  • Curriculum Vitae,
  • degree documents (for any completed degree) and transcript of records (including completed courses and grades) to support that you’re qualified for admission to education at the PhD level,
  • list of publications (if any),
  • copy of your master thesis, or a detailed description of the ongoing thesis work copy, including a plan for its completion, if not fully complete at the end of the application period,
  • list of reference persons with contact details,
  • any other supporting documentation demonstrating your suitability for the position.

It is not a strict requirement for the relevant pre-requisite degree to be completed when the application is made. All applicants should state when they would be able to fulfill all requirements and be ready to assume the position. Given current circumstances, a remote work arrangement might be possible for a starting period.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

Salary: According to local agreement for PhD students.
Starting date: As soon as possible or as otherwise agreed.

Type of employment: Temporary position according to the Higher Education Ordinance chapter 5 § 7.

Scope of employment: 100 %

For further information about the position please contact: Project leader associate professor Carl Nettelblad,, head of division Emanuel Rubensson

Please submit your application by 31 May 2021, UFV-PA 2021/1543.

Are you considering moving to Sweden to work at Uppsala University? Find out more about what it´s like to work and live in Sweden. 

Please do not send offers of recruitment or advertising services.

Submit your application through Uppsala University's recruitment system.

Placement: Department of Information Technology

Type of employment: Full time , Temporary position longer than 6 months

Pay: Fixed salary

Number of positions: 1

Working hours: 100 %

Town: Uppsala

County: Uppsala län

Country: Sweden

Union representative: ST/TCO
Seko Universitetsklubben

Number of reference: UFV-PA 2021/1543

Last application date: 2021-05-31

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